nvnieuwk 6d10909e9f Update tests/modules/ensemblvep/main.nf ... Co-authored-by: Maxime U. Garcia <maxime.garcia@scilifelab.se>		2022-06-09 11:55:41 +02:00
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abacas
abricate
adapterremoval
adapterremovalfixprefix
agrvate
allelecounter
amplify/predict
amps
amrfinderplus
antismash	Apply suggestions from code review	2022-05-12 15:28:19 +02:00
arriba	update md5sum	2022-05-09 15:19:16 +02:00
artic
ascat
assemblyscan
ataqv/ataqv
bakta
bamaligncleaner
bamcmp
bamtools	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
bamutil/trimbam
bandage/image
bbmap
bcftools	fix test	2022-06-08 14:48:16 +02:00
bclconvert
bedtools	added bedtools split	2022-05-17 14:24:32 +02:00
biobambam	fix config	2022-05-17 09:09:19 +02:00
biscuit
bismark
blast
bowtie
bowtie2	add PE sorted test	2022-05-13 19:16:50 +02:00
bracken/bracken
busco	remove 'auto' test	2022-05-06 13:33:27 +00:00
bwa
bwamem2
bwameth
cat
cellranger
centrifuge
checkm/lineagewf
chromap
clonalframeml
cmseq/polymut
cnvkit	added fasta_fai as input + changed if statements	2022-06-02 12:57:50 +02:00
cnvpytor	combine multiple pytor	2022-05-05 23:59:12 +02:00
controlfreec
cooler
csvtk
custom	tests: add missing paths to config	2022-05-11 18:17:27 +02:00
cutadapt
damageprofiler
dastool
dedup
deeparg
deeptools	changed container + add cram2bam conversion	2022-06-02 10:38:05 +02:00
deepvariant
delly/call
diamond	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
dragmap
dragonflye
dshbio
ectyper
elprep	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
emmtyper
ensemblvep	Update tests/modules/ensemblvep/main.nf	2022-06-09 11:55:41 +02:00
expansionhunter
faqcs
fargene
fastani
fastp
fastqc
fastqscan
fasttree
fgbio
filtlong	Fix config for tests	2022-05-31 20:07:52 +02:00
flash
freebayes
gamma/gamma	fixed test.yml	2022-05-24 19:27:09 -04:00
gatk	Add GATK indelrealigner tests	2022-06-08 21:14:08 +02:00
gatk4	add versions.yml	2022-06-07 14:38:43 +02:00
genmap
genomescope2	Update tests/modules/genomescope2/test.yml	2022-05-13 11:27:42 +02:00
genrich
gffread
glnexus
graphmap2
gstama
gtdbtk/classifywf
gubbins
gunc
gunzip
hamronization
happy	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
hicap
hifiasm
hisat2
hmmcopy
hmmer
hmtnote	Update main.nf	2022-05-16 15:20:15 +00:00
homer
hpsuissero
ichorcna
idr
imputeme/vcftoprs
iqtree
ismapper
isoseq3
ivar
jupyternotebook
kaiju
kallisto/index
kallistobustools
kat/hist	Update tests/modules/kat/hist/test.yml	2022-05-23 08:51:49 +02:00
khmer/normalizebymedian
kleborate
kraken2/kraken2
krona	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
last
leehom
legsta
lima
lissero
lofreq
macrel/contigs
macs2/callpeak
mafft
malt
maltextract
manta
mapdamage2
mash	Patch mash screen	2022-05-25 12:29:14 +00:00
mashtree
maxbin2
maxquant/lfq
md5sum	new module: md5sum	2022-05-06 09:20:40 +02:00
medaka
megahit
megan/rma2info
meningotype
meryl	Merge branch 'master' into meryl_unionsum	2022-05-09 16:16:08 +02:00
metabat2
metaphlan3
methyldackel
minia
miniasm
minimap2
mlst
mobsuite/recon
mosdepth	Update main.nf	2022-05-25 19:38:12 +01:00
motus	Update tests/modules/motus/profile/test.yml	2022-05-12 20:55:54 +01:00
msisensor
msisensorpro
mtnucratio
multiqc	formatting	2022-06-08 14:42:58 +02:00
mummer
muscle
nanolyse
nanoplot
ncbigenomedownload
nextclade
ngmaster
ngscheckmate/ncm
nucmer
optitype
pairix
pairtools
panaroo/run
pangolin
paraclu
pbbam/pbmerge
pbccs
peddy
phantompeakqualtools
phyloflash
picard	fix tests (again)	2022-05-22 06:54:09 +02:00
pirate
plasmidid
plink
plink2
pmdtools/filter
porechop
preseq
prinseqplusplus
prodigal
prokka
pycoqc
pydamage
qcat
qualimap
quast
racon
rapidnj
rasusa
raven
raxmlng
rgi/main
rhocall/annotate	update test	2022-06-08 16:36:02 +02:00
rmarkdownnotebook
roary
rsem
rseqc
rtgtools/vcfeval	Small update on the output channels	2022-05-10 12:34:52 +02:00
salmon
samblaster
samtools	Generalize Bam2Cram do either conversion	2022-05-09 15:22:54 +02:00
scoary
seacr/callpeak
seqkit
seqsero2
seqtk
sequenzautils
seqwish/induce
shasum	added sha256sum	2022-05-06 10:28:14 +02:00
shigatyper	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
shovill
sistr
slimfastq	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
snapaligner	fix tags	2022-05-06 18:57:17 +02:00
snippy/run	make prettier	2022-05-11 18:00:36 +00:00
snpdists
snpeff
snpsift/split
snpsites
sourmash/sketch
spades
spatyper
sratools	refactor: move files to custom section	2022-05-11 17:33:45 +02:00
srst2/srst2	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
ssuissero
stadeniolib/scramble
staphopiasccmec
star	Fix tests	2022-05-27 12:14:10 +01:00
stranger
strelka
stringtie
subread/featurecounts
svdb
tabix	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
tbprofiler/profile
tiddit	add test + fix issues	2022-06-03 15:51:02 +02:00
transdecoder
trimgalore
ucsc
ultra/pipeline
umitools	Fix Conda tests	2022-05-23 22:39:12 +01:00
unicycler
untar	fix untar output dir	2022-06-02 11:09:55 +02:00
unzip
vardictjava	Merge remote-tracking branch 'origin' into motus_profile	2022-05-05 09:41:13 -04:00
variantbam
vcfanno
vcflib/vcfuniq
vcftools
vsearch/usearchglobal	prettier	2022-05-30 13:35:12 +02:00
yara